I used to use Metagross almost religiously, until I realized a substantial problem with it - it has terrible moveset syndrome. Meteor Mash, Earthquake, Thunderpunch, Ice Punch, Agility, Explosion, Grass Rope, Pursuit... it really likes having all of these around, and unfortunately, it just can't.
It also doesn't fill many holes... if you scan the threats list, how many of them wield Earthquake or a Fire move, or just plain blast Metagross (see: Heracross)? There's also problems with both Jibacoil and Dugtrio...